scholarly journals Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA

2019 ◽  
Vol 5 (2) ◽  
pp. 38 ◽  
Author(s):  
Yelyzaveta Shlyakhtina ◽  
Katherine L. Moran ◽  
Maximiliano M. Portal
Keyword(s):  
Cell Fate ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
General Pattern ◽  
Nuclear Architecture ◽  
Biological Information ◽  
Current Evidence ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Wide Range

During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.

scholarly journals The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1229
Author(s):  
David Salgado ◽  
Irina M. Armean ◽  
Michael Baudis ◽  
Sergi Beltran ◽  
Salvador Capella-Gutierrez ◽  
...  
Keyword(s):  
Copy Number ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
Genetic Diseases ◽  
White Paper ◽  
Copy Number Variations ◽  
Direct Result ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Definition Of

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

scholarly journals Fast sequence-based microsatellite genotyping development workflow

2019 ◽  
Author(s):  
Olivier Lepais ◽  
Emilie Chancerel ◽  
Christophe Boury ◽  
Franck Salin ◽  
Aurélie Manicki ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
De Novo ◽  
Microsatellite Genotyping ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Genomic Resource ◽  
Analytical Frameworks ◽  
Different Levels

AbstractApplication of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

scholarly journals Genomics Insights: Inter-Laboratory Variability in Array-Based RNA Quantification Methods

2013 ◽  
Vol 6 ◽  
pp. GEI.S11909
Author(s):  
Victoria Y. Wong ◽  
Manuel X. Duval
Keyword(s):  
Large Fraction ◽  
State Level ◽  
Measurement Procedure ◽  
Subsequent Treatment ◽  
Biological Information ◽  
Dna Arrays ◽  
Ribonucleic Acids ◽  
Rna Molecules ◽  
Wide Range ◽  
The Stability

Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. The short half-life property, inherent to RNA, benefits cells that do not need to express their entire repertoire of proteins. The cellular machinery turns off the production of a given protein by shutting down the transcription of its cognate coding gene and by either actively degrading the remaining mRNA or allowing it to decay on its own. The steady-state level of each mRNA in a given cell varies continuously and is specified by changing kinetics of synthesis and degradation. Because it is technically possible to simultaneously measure thousands of nucleic acid molecules, these quantities have been studied by the life sciences community to investigate a range of biological problems. Since the RNA abundance can change according to a wide range of perturbations, this makes it the molecule of choice for exploring biological systems; its instability, on the other hand, could be an underestimated source of technical variability. We found that a large fraction of the RNA abundance originally present in the biological system prior to extraction was masked by the RNA labeling and measurement procedure. The method used to extract RNA molecules from cells and to label them prior to hybridization operations on DNA arrays affects the original distribution of RNA. Only if RNA measurements are performed according to the same procedure can biological information be inferred from the assay read out.

scholarly journals IRE1α Signaling Pathways Involved in Mammalian Cell Fate Determination

2016 ◽  
Vol 38 (3) ◽  
pp. 847-858 ◽  
Author(s):  
Jie Wu ◽  
Guang-Ting He ◽  
Wei-Jin Zhang ◽  
Jing Xu ◽  
Qiao-Bing Huang
Keyword(s):  
Er Stress ◽  
Cell Fate ◽  
Mammalian Cells ◽  
Ring Finger ◽  
Unfolded Protein ◽  
Wide Range ◽  
Functional Relevance ◽  
Cellular Stresses ◽  
Context Specific ◽  
Shock Proteins

A diverse array of cellular stresses can lead to accumulation of misfolded or unfolded proteins in endoplasmic reticulum (ER), which subsequently elicits ER stress. Inositol-requiring enzyme 1α (IRE1α) is the most sensitive of the three unfolded protein response (UPR) branches which are triggered to cope with ER stress in mammalian cells. IRE1α signaling is quite context-specific on account of many adaptor and modulator proteins that directly interact with it, including heat shock proteins (HSPs), RING finger protein 13 (RNF13), poly (ADP-ribose) polymerase 16 (PARP16), Bax/Bak, and Bax inhibitor-1 (BI-1). The activated IRE1α triggers different downstream pathways depending on the UPRosome formed by distinct modulator proteins. At the initial phase of ER stress, IRE1α-XBP1 axis functions as an adaptive response. While ER stress sustains or intensifies, signals shift to apoptotic responses. Furthermore, IRE1α signaling can be exploited to the development of a wide range of prevalent human diseases, with cancer the most characterized. Here we provide an overview of recent insights into the complex IRE1α signaling network which makes IRE1α an intriguing cell fate switch. Besides, the functional relevance is presented since IRE1α activation also participates in some other physiological processes beyond protein-folding status.

scholarly journals Designing Efficient Spaced Seeds for SOLiD Read Mapping

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Laurent Noé ◽  
Marta Gîrdea ◽  
Gregory Kucherov
Keyword(s):  
High Throughput Sequencing ◽  
Color Space ◽  
Major Advance ◽  
Read Mapping ◽  
Sequencing Technologies ◽  
Reading Errors ◽  
Spaced Seeds ◽  
Algorithmic Solution ◽  
Wide Range ◽  
Genomic Studies

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

2020 ◽  
Author(s):  
Simon Poirier ◽  
Sébastien Déjean ◽  
Cédric Midoux ◽  
Kim-Anh Lê Cao ◽  
Olivier Chapleur
Keyword(s):  
Anaerobic Digestion ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
List Type ◽  
Community Patterns ◽  
Microbial Indicators ◽  
Sequencing Technologies ◽  
External Data ◽  
Wide Range ◽  
Process Failure

AbstractAnaerobic digestion (AD) is a microbial process that can efficiently degrade organic waste into renewable energies such as methane-rich biogas. However, the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds, leading to process failure and economic losses. High-throughput sequencing technologies enable the identification of microbial indicators of digesters inhibition and can provide new insights into the key phylotypes at stake during AD process. But yet, current studies have used different inocula, substrates, geographical sites and types of reactors, resulting in indicators that are not robust or reproducible across independent studies. In addition, such studies focus on the identification of a single microbial indicator that is not reflective of the complexity of AD. Our study proposes the first analysis of its kind that seeks for a robust signature of microbial indicators of phenol and ammonia inhibitions, whilst leveraging on 4 independent in-house and external AD microbial studies. We applied a recent multivariate integrative method on two-in-house studies to identify such signature, then predicted the inhibitory status of samples from two datasets with more than 90% accuracy. Our study demonstrates how we can efficiently analyze existing studies to extract robust microbial community patterns, predict AD inhibition, and deepen our understanding of AD towards better AD microbial management.HighlightsRobust biomarkers of AD inhibition were tagged by integrating independent 16S studiesIncrease of the Clostridiales relative abundance is an early warning of AD inhibitionCloacimonetes is associated with good performance of biomethane productionMultivariate model predicts ammonia inhibition with 90% accuracy in external data

scholarly journals Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 49 ◽  
Author(s):  
Shaili Johri ◽  
Michael Doane ◽  
Lauren Allen ◽  
Elizabeth Dinsdale
Keyword(s):  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Vertebrate Species ◽  
Design And Implementation ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Population Structures ◽  
Genomic Studies ◽  
Species Groups ◽  
Data Deficient

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.

scholarly journals In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species

Data ◽  
2020 ◽  
Vol 5 (4) ◽  
pp. 111
Author(s):  
Arman Kulyyassov ◽  
Ruslan Kalendar
Keyword(s):  
High Throughput ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Regulatory Elements ◽  
Scoring Method ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Multiple Species ◽  
Eukaryotic Organisms ◽  
The Impact

High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.

scholarly journals RNAsamba: coding potential assessment using ORF and whole transcript sequence information

2019 ◽  
Author(s):  
Antonio P. Camargo ◽  
Vsevolod Sourkov ◽  
Marcelo F. Carazzolle
Keyword(s):  
High Throughput Sequencing ◽  
Model Organisms ◽  
Sequence Information ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Partial Length ◽  
Non Coding Rnas ◽  
Coding Potential

AbstractMotivationThe advent of high-throughput sequencing technologies made it possible to obtain large volumes of genetic information, quickly and inexpensively. Thus, many efforts are devoted to unveil the biological roles of genomic elements, being one of the main tasks the identification of protein-coding and long non-coding RNAs.ResultsWe describe RNAsamba, a tool to predict the coding potential of RNA molecules from sequence information using a deep-learning model that processes both the whole sequence and the ORF to look for patterns that distinguish coding and non-coding RNAs. We evaluated the model in the classification of coding and non-coding transcripts of humans and five other model organisms and show that RNAsamba mostly outperforms other state-of-the-art methods. We also show that RNAsamba can identify coding signals in partial-length ORFs and UTR sequences, evidencing that its model is not dependent on the presence of complete coding regions. RNAsamba is a fast and easy tool that can provide valuable contributions to genome annotation pipelines.Availability and implementationThe source code of RNAsamba is freely available at:https://github.com/apcamargo/RNAsamba.

scholarly journals Fast sequence-based microsatellite genotyping development workflow

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9085 ◽  
Author(s):  
Olivier Lepais ◽  
Emilie Chancerel ◽  
Christophe Boury ◽  
Franck Salin ◽  
Aurélie Manicki ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
De Novo ◽  
Microsatellite Genotyping ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Genomic Resource ◽  
Analytical Frameworks ◽  
Different Levels

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20–40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

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